1. angela lansbury last performance
/
2. gorilla stone bloods paperwork
/
3. worst places to live in oregon
/
4. error: package or namespace load failed for 'deseq2

error: package or namespace load failed for 'deseq2

Loading required package: GenomicRanges Policy. Error: package or namespace load failed for 'olsrr' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): there is no package called 'zip' mara May 25, 2021, 12:49pm #2 It looks like you need a package that it depends on. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. error: object 'rlang_dots_list' not found Policy. When an R package depends on a newer package version, the required package is downloaded but not loaded. Finally After 3-4 manual installations of missing packages everything worked. Installing package(s) 'XML' If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: I am also encountering a set of similar (although possible totally unrelated) issue with other packages, RStudio provides the following warning every startup, library(devtools) gives the following errors, Someone on twitter asked for the results of packageDescription("rlang"). Also make sure that you have RTools.exe installed and working. Find centralized, trusted content and collaborate around the technologies you use most. I tried following the instructions for 2019.7 as well and I am getting the same error. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Hey, I tried your suggestion and it didn't work as it is but I did figure it out probably with the help of your suggestion. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? Connect and share knowledge within a single location that is structured and easy to search. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? What is a word for the arcane equivalent of a monastery? MathJax reference. R version 3.6.1 (2019-07-05) How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? rev2023.3.3.43278. In addition: Warning message: [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 Policy. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 Running under: Windows 10 x64 (build 18362), locale: unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Policy. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 This sort of problems almost always comes from a bug in R on Windows: If you reinstall a package that includes compiled code, and if that package is already loaded in R, the DLL will not get updated. If I run install.packages(GenomeInfoDb) from R console, it is telling me that the package is not available for R version 3.5.1. March 1, 2023, 3:25pm Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. One solution is to find all available packages. library ("DESeq2") Error: package or namespace load failed for 'DESeq2' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): there is no package called 'Hmisc' Installing Hmisc as suggested above did not solve the issue. May I know is there any other approach I can try? If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. Well occasionally send you account related emails. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 As such there are two solutions that may be more or less attainable given your own IT system. Styling contours by colour and by line thickness in QGIS. install.packages ("zip") Should I update the Bioconductor to latest version instead? C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages How do I align things in the following tabular environment? failed UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: Specifications: q2-aldex2 -> python=3.6 Your python: python=3.8.15 Update all/some/none? 9543 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}, The downloaded source packages are in Following successful installation of backports BiocManager::install ("DESeq2") will succeed under [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 Sorry, I'm newbie. Try again and choose No. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). Please read the posting Join us at CRISPR workshops in Koper, Slovenia in 2023. It is working now. Loading required package: GenomeInfoDb I'm trying to reproduce your problem, so being as precise as possible is important. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 When you install and load some libraries in a notebook cell, like: While a notebook is attached to a cluster, the R namespace cannot be refreshed. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). there is no package called GenomeInfoDbData I've copied the output below in case it helps with troubleshooting. Platform: x86_64-w64-mingw32/x64 (64-bit) Error: package or namespace load failed for 'DESeq2' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): there is no package called 'locfit' 0 cbravo11 0 @e0025e70 Last seen 10 months ago United States I installed DESeq2 using this code: Warning: restored xfun, The downloaded binary packages are in Sign up for a free GitHub account to open an issue and contact its maintainers and the community. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 there is no package called GenomeInfoDbData Is a PhD visitor considered as a visiting scholar? [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 I hope you can see something I can't see and help me solving this issue. in your system, start R and enter: Follow Warning message: Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide, You can try installing packages in R (which comes with R 3.5.1, not RStudio). Error: package or namespace load failed for ggplot2 and for data.table, Error: package or namespace load failed for car, Error: package or namespace load failed for rJava, Error in load Namespace, object 'vI' not found with package AnnotationDbi. Idk, but the issue came up from using installations from within R/Rstudio, and maybe it will never happen if we use just, @NikitaVlasenko you should be able to point Rstudio to the, We've added a "Necessary cookies only" option to the cookie consent popup, DESeqDataSetFromTximport invalid rownames length, deseq2 model design : Different gene output, deseq2 single factor design output interpretation. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Installing DESeq2 Error: no package called GenomeInfoDbData, https://bioconductor.org/packages/3.11/data/annotation/src/contrib/GenomeInfoDbData_1.2.3.tar.gz, https://cran.rstudio.com/bin/macosx/contrib/4.0/RcppArmadillo_0.9.880.1.0.tgz, https://cran.rstudio.com/bin/macosx/contrib/4.0/survival_3.1-12.tgz. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Old packages: 'RcppArmadillo', 'survival' Convince your IT department to relax the permissions for R packages I'm having a similar error, but different package: library("DESeq2") While a notebook is attached to a cluster, the R namespace cannot be refreshed. If you try loading the DEseq2 library now, that might work. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 Is a PhD visitor considered as a visiting scholar? nnet, spatial, survival. there is no package called Hmisc. I tried again and again was met with missing packages BUT!!! How to use Slater Type Orbitals as a basis functions in matrix method correctly? downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Retrying with flexible solve.Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.Collecting package metadata (repodata.json): doneSolving environment: failed with initial frozen solve. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Error: package or namespace load failed for 'GenomeInfoDb' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called 'GenomeInfoDbData' Error: package 'GenomeInfoDb' could not be loaded I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. Connect and share knowledge within a single location that is structured and easy to search. Remember to always click on the red Show me the content on this page notice when navigating these older versions. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 Browse other questions tagged, Start here for a quick overview of the site, Detailed answers to any questions you might have, Discuss the workings and policies of this site. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Does anyone know why I'm getting the following message when I load tidyverse in a new session. Warning: cannot remove prior installation of package xfun [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( Language(R, Python, SQL) now when I tried installing the missing packages they did install. Use MathJax to format equations. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. How do you ensure that a red herring doesn't violate Chekhov's gun? [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 rev2023.3.3.43278. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): and then updating the packages that command indicates. May be the version has problem How can I do ? "After the incident", I started to be more careful not to trip over things. @KonradRudolph It's pacman (not packman) and you are correct in that it's basically just a wrapper for, Thanks for your suggestion, I tried doing this step by step as you said but the biocLite command still did throw errors for missing packages. [5] IRanges_2.8.1 S4Vectors_0.12.1 I noticed that you are trying to install qiime2-2019.4, this may not work as ALDEx2 was made for qiime2-2019.7 as outlined here, up to and including the versions I mentioned earlier. Content type 'application/zip' length 233860 bytes (228 KB) Hello, Thanks for your suggestion. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Is there anyone the same as mine error while loading library(DESeq2)? Bioconductor release. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. That plugin is has not been updated to work with later releases of QIIME 2. so I would try to use BiocManager::install("XML"). [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 I would like to install DESeq2 for DE analysis. I am running a new install of R (3.5.0) and RStudio (1.1.414). Glad everything is finally working now. Traffic: 307 users visited in the last hour, https://cran.rstudio.com/src/contrib/htmlTable_2.1.0.tar.gz', https://wbc.upm.edu.my/cran/src/contrib/PACKAGES'. What am I doing wrong here in the PlotLegends specification? there is no package called data.table Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Id also remove and re-install the version of QIIME 2 you tried to force install an older version of python, as you can tell, many things just broke. Installing packages directly into that location fixes the issue but is not desirable for all the reasons that people might want to use custom locations (e.g. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Please try reinstalling rlang on a fresh session. Thank you @hharder. .onLoad failed in loadNamespace() for 'rlang', details: /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages In file.copy(savedcopy, lib, recursive = TRUE) : Use of this site constitutes acceptance of our User Agreement and Privacy survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Surly Straggler vs. other types of steel frames. This is the same answer I wrote in a comment to Hack-R I just wanted to post a separate answer: What I did was - uninstalled everything (RTools then RStudio thenR and also I deleted the R directory because it still had all the previous libraries) I did this in order to eliminate any chance that something was corrupt. [13] ggplot23.3.0 car3.0-7 carData3.0-3 You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. I would suggest to install data.table, lme4 and all of the packages denoted in the 2 statements that said Packages which are only available in source form, and may need compilation of C/C++/Fortran: with pacman then re-run the Bioconductor installation of your target package. package in your R session. [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. Installing package(s) 'htmlTable', 'xfun' Please try the following steps: Quit all R/Rstudio sessions. I installed the package successfully with conda, but Rstudio is apparently does not know about it. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 How to notate a grace note at the start of a bar with lilypond? No error messages are returned. I was assuming that to be the case. If you preorder a special airline meal (e.g. Are there tables of wastage rates for different fruit and veg? Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Solution To resolve this error, install the required package as a cluster-installed library. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. Use of this site constitutes acceptance of our User Agreement and Privacy We've tried this - and can replicate this issue on a completely new install with no existing package installs. [Note I have now updated to 3.5.1 and 1.1.453 and am still experiencing the issues below with the exception of the "built under R version 3.5.1" warning messages], I have installed the rlang package using install.packages("rlang") without encountering any issues but when I attempt to load the package I get the following error, Error: package or namespace load failed for rlang: [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . enter citation("DESeq2")): To install this package, start R (version I would recommend installing an older version of QIIME 2 for this plugin to work. biocLite(), install.packages() (and the devtools equivalent?) First the biocLite (the installer of all the related packages, on the previous installation of the DESeq2 package everything was smooth but it was on Linux), Then trying to install the DESeq2 package with biocLite (looks like everything is good). By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. "4.2") and enter: For older versions of R, please refer to the appropriate Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. to one of the following locations: https://code.bioconductor.org/browse/DESeq2/, https://bioconductor.org/packages/DESeq2/, git clone https://git.bioconductor.org/packages/DESeq2, git clone git@git.bioconductor.org:packages/DESeq2. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Just to add on -- do you require an old version of Bioconductor for your current project? [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Policy. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) I am using the latest stable LAMMPS version (updated 17th Feb 2023) Also I am having troubles with the CMAKE unit testing, in particular for the force styles. Learn more about Stack Overflow the company, and our products. This is default text for notification bar, Removing Unwanted Variation Using Pseudoreplicates and Pseudosamples, Identifying Differentially Abundant Phosphoproteome Sites With ProteomeRiver, Extension of scPipe Bioconductor Package for scATAC-seq Data, Matilda for Single-cell Multi-omics Data Integration, cellXY for Exploring Gender-specific Genes in Single Cell RNA-seq Data, Stereopy as an Advanced Tool for Interpreting Spatial Transcriptomics Data, Spectre Toolkit for Rapid Analysis of Cytometry Data, A Bioconductor Framework for High-dimensional in situ Cytometry Analysis, Error when installing Aldex2 Community Plugin Support, How the Gut Microbiota Affects COVID-19 Vaccine Immunogenicity , Clinical Application of 24 G Cannula Needle and 3-0 Polypropylene Suture in Vas Deferens Exploration. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Then I reinstalled R then Rstudio then RTools. Sounds like there might be an issue with conda setup? I'm running into some bad problems installing and using the DESeq2 package for R. I freshly installed R 3.3.1 and Rstudio 0.99.903 on Win7. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Open Source Biology & Genetics Interest Group. Is there a single-word adjective for "having exceptionally strong moral principles"? Assuming that your conda environment name is renv, try running this in the terminal: This should open up the Rstudio interface, like normal, but using everything defined in your renv environment. If not fixed, Try removing remove.packages (rlang) then. Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' Error: package or namespace load failed for 'DESeq2' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): 'KEGGREST' 2301_76497647 17 1 109+ 20+ 30 10 1 0 2 0 Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") 1. Any suggestions would be greatly appreciated. Asking for help, clarification, or responding to other answers. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. install.packages("BiocManager"), I get this error: [7] edgeR_3.16.5 limma_3.30.12 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Is the God of a monotheism necessarily omnipotent? R version 4.0.1 (2020-06-06) I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Thanks for contributing an answer to Stack Overflow! Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. Looking for incompatible packages.This can take several minutes. Making statements based on opinion; back them up with references or personal experience. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 By clicking Sign up for GitHub, you agree to our terms of service and Why is this sentence from The Great Gatsby grammatical? call: dots_list() Did you do that? Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Press CTRL-C to abort. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called locfit, Traffic: 307 users visited in the last hour, https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages, User Agreement and Privacy Thanks for contributing an answer to Stack Overflow! I tried installing DESeq2 using: but it run into a lot of errors (some missing packages for some dependency packages etc) Then I tried installing all the missing packages manually by downloading from CREN and installing the missing packages from .zip files. It only takes a minute to sign up. To learn more, see our tips on writing great answers. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Documentation package rlang was built under R version 3.5.1. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Choose Yes. . Whats the grammar of "For those whose stories they are"? Running under: macOS Sierra 10.12.3, locale: 9. Press CTRL-C to abort.failedUnsatisfiableError: The following specifications were foundto be incompatible with the existing python installation in your environment:Specifications: It also hung on the solving environment for over an hour. Making statements based on opinion; back them up with references or personal experience. Powered by Discourse, best viewed with JavaScript enabled, DESeq2: Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. I can download DESeq2 using, User Agreement and Privacy Sounds like you might have an issue with which R Rstudio is running. Erasmus+ funds available! I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. "htmlTable", "xfun" Surly Straggler vs. other types of steel frames. But I guess you have many problems with your installation, and I'd suggest. I tried to get a whole new environment and install an old version of Qiime but I still got a ton of conflicts and it didnt install. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Installing package(s) 'GenomeInfoDbData' Retrying with flexible solve.Solving environment: Found conflicts! Feedback In the Bioconductor realm, I would then check that package versions are consistent with the version of Bioconductor in use, and would ask more Bioconductor-related questions on the Bioconductor support site. To learn more, see our tips on writing great answers. binary source needs_compilation * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc From the console install.packages ("rlang") should fix this. As mentioned above, my institutional IT can replicate this on a laptop with a completely fresh R install and no prior package installations (meaning isn't to do with installing with another version of the package already running).

Pompa Iron Resurrection Net Worth, Playa Del Ingles To Puerto Rico, Articles E